5 Easy Steps to PDB Deposition with OneDep

1

Check Sample
Sequence

Sequence should• Contain all residues• Include expression tags
and disordered residues
Check against reference
database with BLAST• Proteins [UniProt BLAST• Nucleic acids [NCBI BLAST!

2

CheckLigands

Are your ligands already in
our Chemical Component
Dictionary (CCD)?
Check at:• Ligand Expoligand-expo.rcsb.org• PDBeChempdbe.org/chem• Chemie search
pdbj.org/chemie-search
Is the ligand present
in the CCD?

Any mismatchshould correspond tomutation, variant orexpression tag inyour sequence.

Yes The 3-charactercode for yourligand shouldmatch that in thedictionary

Example of a UniProtalignment with highlighted
mismatch

No During deposition
you can provide a
SMILES or uploada 2D chemical
diagramQuery
61 RWWANDGRTPGSR

3Prepare Data

Generate coordinate file in
PDBx/mmCIF format• This can be output directlyfrom some refinement
programs(e.g., PHENIX, REFMAC)• This ensures that themaximum metadata iscaptured from the file fordeposition
pdb_extract can be usedto extract information.
Visit pdb-extract.wwpdb.org• Creates single PDBx/
mmCIF file containing
extra meta data (e.g.,author info,data collection andrefinement stats) using
output log files• Converts SF files to PDBx/
mmCIF format for
non-MTZ format files

Example of a chemical
diagram that should beprovided at depositionRWW NDGRTPGSR
79 RWWCNDGRTPGSR
P00698(UniProt Sequence)

Depending on the depositor’s geographical location, the structure will be assigned for processing
to one of the worldwide Protein Data Bank sites: RCSB PDB, PDBe, or PDBj.

AfterDeposition
3 Validate!
PrepareDataValidate!
for Deposition

45

The wwPDB provides a
standalone validation server
for checking your structure
Visit validate.wwpdb.org

Deposition to the OneDep
system can be carriedout at the wwPDB
deposition pages.
Visit deposit.wwpdb.org• Both model and experimental data are validated• Provides detailed reports(PDF and XML files)! Attempt to fix major

issues highlighted prior
to deposition to minimize
the requirement forreplacement files. It will
reduce the time needed
to process your entry.

Deposit yourstructure

Deposition is tailored toexperimental type:• X-ray, Neutron, NMR,
EM, or any combinationof these• You must upload therelevant coordinate andexperimental data files
and include mandatory
information
A session ID is provided toenable you to continue yourdeposition at a later date.
A PDB ID will be provided
upon completion of yourdeposition.

Entries are annotated,validated, and returned
to authors for review• Processed files andofficial validation report
can be downloaded atcommunication page
Request entry release andprovide citation publication
information using OneDep’s
communication panel.
Coordinate release follows
instructions given atdeposition• REL - released immediately
after processing• HPUB - hold until
publication, up to 1 year
• HOLD - hold up to 1 year
If the structure is not
published within 1 year, youhave the option to either
release or withdraw the entry.

Deposition Checklist

Online resources
PDB_extract: pdb-extract.wwpdb.org
Validation: validate.wwpdb.org
Deposition: deposit.wwpdb.org

4 Check sample sequenceq
Refer to UniProt

4 Check ligandsq
Are these correctly assigned?

4 Prepare data for depositionq

Generate PDBx/mmCIF-formatted data
files to provide the most complete
information about your structure

4 Validate your dataq
Use wwPDB’s standalone
validation service

4 Deposit your structure usingq
OneDep System
When you are ready

Further Information
Tutorials and FAQs for validation and deposition
can be found at:www.wwpdb.org/validation/validation-reports
wwpdb.org/deposition/tutorial
wwpdb.org/deposition/faq

STEPS

DEPOSITION

Contact Information
validation@mail.wwpdb.org
deposit-help@mail.wwpdb.org

Citation Information
Cite wwPDB:Nature Structural Biology 10, 980 (2003)
doi: 10.1038/nsb1203-980
Cite OneDep:
Structure 25, 536-545 (2017)
doi: 10.1016/j.str.2017.01.004

wwPDB Members

PDB ID5a1a5TO PDB
EASY

wwPDB.org

wwpdb.org

PDB ID1d1i